SMTL ID : 5te3.1 (1 other biounit)

Crystal structure of Bos taurus opsin at 2.7 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 5 residues within 4Å: Chain A: F.220, K.231, T.251, V.254, I.255 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.220, A:T.251, A:V.254, A:I.255 Hydrogen bonds: A:K.231 Salt bridges: A:K.231 BOG.3: 5 residues within 4Å: Chain A: P.27, Y.96, L.99, H.100, Y.102 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.96, A:L.99 Salt bridges: A:H.100 BOG.8: 13 residues within 4Å: Chain A: A.117, T.118, G.121, C.187, G.188, I.189, Y.191, M.207, F.212, W.265, Y.268, A.269, A.272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.191, A:M.207, A:F.212, A:Y.268, A:A.269, A:A.272 Hydrogen bonds: A:C.187, A:I.189, A:Y.268

2 x PLM: PALMITIC ACID(Covalent)

PLM.4: 3 residues within 4Å: Chain A: C.322, N.326 Ligands: PLM.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.326 PLM.7: 4 residues within 4Å: Chain A: L.321, C.322, C.323 Ligands: PLM.4 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: Q.36, I.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 SO4.6: 1 residues within 4Å: Chain A: Q.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.237, A:Q.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulati, S. et al., Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-15

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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